Table 2.
Enrichment of functional categories among the commonly regulated genes in wild-type and mutant plants as a response to LL/HL transfer at t 4h versus t 0 and t 48h versus t 0The threshold of log2 ratios was kept at ±1.5. Only functional categories with five or more altered genes are displayed.
| Functional categories | No. of commonly regulated genes | |||
|---|---|---|---|---|
| t 4h versus t 0 | t 48h versus t 0 | |||
| Up-regulated | Down-regulated | Up-regulated | Down-regulated | |
| Cell wall | – | 16 (2.65)* | – | 11 (3.05)* |
| Development | 9 (1.12) | 7 (0.85) | 5 (2.58) | 5 (1.02) |
| DNA synthesis/chromatin structure | 9 (0.96) | – | – | |
| Hormone metabolism | 5 (0.87) | 13 (2.20)* | – | 14 (3.96)* |
| Lipid metabolism | 7 (1.54) | 10 (2.15)* | – | 7 (2.51)* |
| Major CHO metabolism | 11 (8.87)* | – | – | – |
| Misc. – Cytochrome P450 | 5 (2.01) | – | – | – |
| Misc. – (UDP glucosyl- and glucoronyl transferases) | 5 (2.48) | – | – | – |
| Protein – degradation | 11 (0.59)* | 21 (1.10) | – | 10 (0.88) |
| Protein – post-translational modification | – | 10 (1.18) | – | 6 (1.18) |
| Protein – synthesis | 8 (1.24) | – | – | – |
| Protein – targeting | 6 (1.97) | – | – | – |
| RNA – processing | 9 (2.89)* | – | – | – |
| RNA – regulation of transcription (RT) | 30 (1.24) | 44 (1.78)* | – | 22 (1.49) |
| Secondary metabolism – flavonoids | 5 (5.18)* | – | 11 (47.32)* | – |
| Signalling | 8 (0.55)* | 21 (1.42) | – | 15 (1.69) |
| Stress – abiotic | 10 (2.16)* | 9 (1.91) | – | 5 (1.77) |
| Stress – biotic | 6 (1.12) | – | – | – |
| Transport | 14 (1.22) | 18 (1.54) | 7 (2.54)* | 11 (1.57) |
The numbers of significantly (P<0.01) altered genes were taken from Supplementary Table S7 available at JXB online.
The threshold of log2 ratios was kept at ±1.5.
The data in parentheses refer to over- or under-represented functional categories (i.e. numbers above or below 1).
Significantly (P<0.05) over- or under-represented categories according to the Fisher’s exact test are marked by an asterisk.
Over-represented categories are shown in bold letters, whereas under-represented categories are in italics.